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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 24828 | 3' | -57.8 | NC_005284.1 | + | 7710 | 0.66 | 0.571523 |
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Target: 5'- --cCUUGCCCGAUGCCcCGua-GACGu -3' miRNA: 3'- cucGAACGGGCUGCGGcGCuugCUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 9887 | 0.66 | 0.560838 |
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Target: 5'- -cGCacccGCCCGGauaGuuGUGAGCGACGg -3' miRNA: 3'- cuCGaa--CGGGCUg--CggCGCUUGCUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 46543 | 0.66 | 0.560838 |
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Target: 5'- -cGuCUUGCCgaGcCGCagCGCGAGCGACAu -3' miRNA: 3'- cuC-GAACGGg-CuGCG--GCGCUUGCUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 930 | 0.66 | 0.539641 |
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Target: 5'- -cGCUgUGCUCGAUGCUgaacugGCGGGCGAUc -3' miRNA: 3'- cuCGA-ACGGGCUGCGG------CGCUUGCUGu -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 33544 | 0.67 | 0.529143 |
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Target: 5'- aAGCUca-CCGcCGCCGCGAGCuGAUAu -3' miRNA: 3'- cUCGAacgGGCuGCGGCGCUUG-CUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 39438 | 0.67 | 0.518722 |
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Target: 5'- cGAGCcaucgGCCUGcACGCCGa--GCGACAc -3' miRNA: 3'- -CUCGaa---CGGGC-UGCGGCgcuUGCUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 9336 | 0.67 | 0.512508 |
|
Target: 5'- cGAGCaacuggucGCCCGAcaaucgcgaCGCCGCGAauaucgucgccggccGCGACu -3' miRNA: 3'- -CUCGaa------CGGGCU---------GCGGCGCU---------------UGCUGu -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 7090 | 0.67 | 0.508383 |
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Target: 5'- cGAGCgcgcgUGCCCuuccuUGCCGUcAGCGGCAu -3' miRNA: 3'- -CUCGa----ACGGGcu---GCGGCGcUUGCUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 23345 | 0.67 | 0.498132 |
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Target: 5'- uGGGg--GCCCGgcGCGCCGC-AGCGGCGc -3' miRNA: 3'- -CUCgaaCGGGC--UGCGGCGcUUGCUGU- -5' |
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| 24828 | 3' | -57.8 | NC_005284.1 | + | 8205 | 0.66 | 0.582256 |
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Target: 5'- cGGCgUUGCCCacuGCGCCGCcaugcuCGGCAa -3' miRNA: 3'- cUCG-AACGGGc--UGCGGCGcuu---GCUGU- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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